Fixing Boolean issues between objects with matching edges/vertices
Okay so I found one way to fix this


Duplicate one of the two offending meshes
Apply remesh to the new duplicate
Separate a part of the mesh that included the offending vertices from the newly remeshed mesh
Delete the offending vertices and vertices that overlay with the new piece from the old mesh
Stitch together the old mesh and the newly remeshed part


The reason I needed to restitch the old mesh with the remeshed piece is because the remesh destroyed edges and faces that didn't fall along the remesh grid (aka curves and diagonals)

Still looking to see if there are simpler/less destructive ways around this though